Contacts of the helix formed by residues 540 - 556 (chain A) in PDB entry 3QFR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A CYS* 4.5 1.6 - - - -
535A GLY 3.3 12.5 + - - +
537A GLY 3.1 17.7 + - - +
538A THR 2.9 2.1 - - - +
539A GLY* 1.3 78.5 - - - +
541A ALA* 1.3 70.0 + - - +
542A PRO 3.5 0.4 - - - -
543A PHE* 3.0 18.3 + - + +
544A ILE* 3.2 22.4 + - + +
565A LEU* 4.2 24.5 - - + -
567A TYR* 3.8 21.5 - - + -
577A LEU* 4.3 11.2 - - + +
578A TYR* 4.3 21.5 - - + -
582A LEU* 4.8 4.7 - - + -
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A SER 3.8 16.4 - - - +
461A ILE 4.2 0.2 - - - -
462A ALA* 3.3 24.1 - - + +
475A CYS* 4.0 21.3 - - + -
538A THR 2.9 16.3 + - - +
539A GLY 3.1 1.2 - - - -
540A VAL* 1.3 80.9 - - - +
542A PRO* 1.3 69.8 - - + +
544A ILE* 3.1 14.0 + - - +
752A FAD 3.8 12.1 - - - +
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Residues in contact with PRO 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A SER* 4.7 1.7 - - - -
320A GLY* 4.8 9.0 - - - +
460A SER* 4.0 12.1 - - - -
461A ILE 3.5 17.0 - - - +
521A PHE* 4.1 26.5 - - + -
539A GLY 3.3 10.8 - - - +
541A ALA* 1.3 95.0 - - + +
543A PHE* 1.3 62.3 + - + +
545A GLY* 3.2 4.5 + - - -
546A PHE* 3.0 29.4 + - + -
632A CYS* 3.4 32.8 - - + -
677A ASP* 4.3 2.5 - - - +
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Residues in contact with PHE 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A PHE* 3.8 22.4 - + - -
533A MET* 3.4 37.0 - - + -
534A VAL 3.5 26.7 - - - -
535A GLY* 3.7 3.8 - - - -
539A GLY 3.7 22.2 - - - -
540A VAL* 3.0 9.5 + - + +
542A PRO* 1.3 76.2 - - - +
544A ILE* 1.3 59.7 + - - +
546A PHE* 3.5 12.3 - + - +
547A ILE* 2.8 38.0 + - + +
565A LEU* 4.1 21.5 - - + -
630A TYR* 3.5 40.6 - - + -
632A CYS* 3.9 7.4 - - + -
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Residues in contact with ILE 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A HIS* 6.0 1.6 - - - +
462A ALA* 3.6 15.7 - - + +
540A VAL* 3.2 28.4 + - + +
541A ALA* 3.1 9.5 + - - +
543A PHE* 1.3 78.4 - - + +
545A GLY* 1.3 60.8 + - - +
547A ILE* 3.6 4.9 + - - +
548A GLN* 2.9 41.8 + - + +
578A TYR* 3.6 54.1 - - + -
581A GLU* 6.0 3.4 - - + -
582A LEU* 4.2 21.5 - - + -
585A PHE* 5.0 8.6 - - + -
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Residues in contact with GLY 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A SER* 3.5 9.5 + - - -
461A ILE 5.4 0.2 - - - -
462A ALA 3.5 8.3 + - - -
463A SER* 3.7 27.6 - - - -
464A SER* 3.3 11.7 - - - -
542A PRO 3.2 7.1 + - - -
543A PHE 3.1 0.2 - - - -
544A ILE* 1.3 79.1 - - - +
546A PHE* 1.3 63.5 + - - +
548A GLN* 3.3 2.1 + - - -
549A GLU* 3.0 19.9 + - - +
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Residues in contact with PHE 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A SER* 3.6 37.5 - - - -
320A GLY* 4.2 2.5 - - - -
521A PHE* 3.7 21.3 - + - -
522A ARG* 4.1 1.8 - - - -
523A LEU* 3.8 42.1 - - + +
531A VAL* 5.8 0.4 - - + -
533A MET* 3.8 17.0 - - + -
542A PRO 3.0 15.8 + - - +
543A PHE* 3.5 30.5 - + - +
545A GLY* 1.3 76.8 - - - +
547A ILE* 1.3 62.8 + - - +
549A GLU* 3.2 2.3 + - - +
550A ARG* 2.9 29.2 + - + +
630A TYR* 3.7 39.9 - + - -
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Residues in contact with ILE 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A MET* 3.3 33.7 - - + -
543A PHE* 2.8 31.5 + - + +
544A ILE* 3.8 7.9 - - - +
546A PHE* 1.3 72.6 - - - +
548A GLN* 1.3 61.0 + - - +
550A ARG* 3.2 6.1 + - + +
551A ALA* 2.9 21.8 + - - +
563A THR* 3.8 6.1 - - + -
565A LEU* 4.9 5.2 - - + -
582A LEU* 4.6 11.0 - - + -
585A PHE* 3.5 42.0 - - + -
590A ALA* 4.8 5.6 - - + +
591A LEU* 3.8 27.8 - - + +
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Residues in contact with GLN 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ALA 4.1 4.9 + - - -
463A SER* 3.6 2.2 - - - +
464A SER* 2.9 30.1 + - - -
467A VAL* 4.1 14.5 - - + +
468A HIS* 3.5 30.9 + - - -
473A HIS* 4.6 5.5 + - - -
544A ILE* 2.9 36.9 + - + +
545A GLY* 3.3 5.4 + - - +
547A ILE* 1.3 75.3 - - - +
549A GLU* 1.3 58.5 + - - +
551A ALA* 3.1 3.5 + - - +
552A TRP* 2.8 30.7 + - - +
585A PHE* 4.0 24.7 - - + -
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Residues in contact with GLU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLU* 4.4 6.1 - - - +
319A SER* 3.4 21.8 + - - -
464A SER* 3.0 26.2 + - - +
465A SER 4.7 0.7 + - - -
466A LYS* 2.9 39.7 + - + +
523A LEU* 3.5 26.5 - - + +
545A GLY 3.0 7.2 + - - +
546A PHE 3.6 7.2 - - - +
548A GLN* 1.3 79.4 - - - +
550A ARG* 1.3 58.1 + - - +
552A TRP* 3.3 9.6 + - + +
553A LEU* 2.9 42.7 + - + +
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Residues in contact with ARG 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A LEU* 4.0 21.0 - - + +
524A PRO* 4.0 19.8 + - - +
527A ALA* 3.4 23.8 + - - +
529A THR 2.7 27.1 + - - -
531A VAL* 3.9 12.1 - - + +
533A MET* 6.1 0.2 - - + -
546A PHE* 2.9 23.5 + - + +
547A ILE* 3.2 6.0 + - + +
548A GLN 3.2 0.2 - - - -
549A GLU* 1.3 76.5 - - - +
551A ALA* 1.3 61.5 + - - +
553A LEU* 3.4 14.5 + - - +
554A ARG* 3.2 28.7 + - - +
560A VAL* 3.4 18.1 - - + +
561A GLY 3.5 14.5 + - - -
562A GLU 3.5 7.1 + - - -
563A THR* 3.1 40.0 + - + +
590A ALA* 5.0 5.6 - - - +
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Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ILE 2.9 14.4 + - - +
548A GLN 3.6 4.5 - - - +
550A ARG* 1.3 74.3 - - - +
552A TRP* 1.3 64.3 + - - +
554A ARG* 3.3 7.0 + - - +
555A GLN* 3.1 35.5 + - - +
585A PHE* 4.0 16.4 - - + -
590A ALA* 3.4 30.4 - - + +
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Residues in contact with TRP 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LYS* 3.7 53.4 + - + -
467A VAL* 3.9 23.3 - - + -
548A GLN 2.8 17.1 + - - +
549A GLU* 3.6 5.2 - - - +
551A ALA* 1.3 78.8 - - - +
553A LEU* 1.3 94.5 + - + +
555A GLN* 3.4 22.5 + - - +
556A GLN* 3.0 66.5 + - + +
558A LYS* 6.3 1.6 - - - -
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Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LYS* 5.8 1.6 - - - +
523A LEU* 5.7 2.5 - - + -
527A ALA* 3.9 25.6 - - + -
549A GLU* 2.9 33.9 + - + +
550A ARG* 3.6 19.7 - - - +
551A ALA 3.2 0.2 - - - -
552A TRP* 1.3 106.5 - - + +
554A ARG* 1.3 65.4 + - - +
556A GLN* 3.4 6.5 + - + +
558A LYS* 3.1 43.5 + - + +
560A VAL* 4.0 11.2 - - + -
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Residues in contact with ARG 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A ARG 3.2 17.8 + - - +
551A ALA* 3.3 6.5 + - - +
553A LEU* 1.3 77.9 - - - +
555A GLN* 1.3 58.0 + - + +
557A GLY* 3.0 20.8 + - - -
558A LYS 3.8 9.5 - - - +
560A VAL* 3.6 26.9 + - + +
588A ASP 3.4 21.4 + - - -
589A GLY* 3.7 17.6 + - - -
590A ALA* 3.6 31.8 - - - +
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Residues in contact with GLN 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A ALA* 3.1 23.6 + - - +
552A TRP* 3.5 29.6 + - - +
553A LEU 3.2 0.2 - - - -
554A ARG* 1.3 73.7 - - + +
556A GLN* 1.3 65.3 + - - +
557A GLY* 2.9 11.2 + - - -
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Residues in contact with GLN 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A TRP* 3.0 63.8 + - + +
553A LEU* 3.4 4.9 + - - +
554A ARG 3.3 0.8 - - - -
555A GLN* 1.3 85.3 + - - +
557A GLY* 1.3 55.8 + - - +
558A LYS* 3.2 35.7 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il